Methods and compositions for modulating gene expression

Abstract

The present disclosure provides compositions with a modulating gene expression and methods for modulating transcription.

What is claimed is: 
     
       1. A chimeric protein, comprising:
 a targeting element comprising a sequence targeting polypeptide that binds in or around an anchor sequence associated with a target anchor sequence-mediated conjunction; and 
 an effector domain comprising all or a biologically active portion of an epigenetic modifying agent, wherein the chimeric protein modifies the anchor sequence associated with the target anchor sequence-mediated conjunction, wherein the target anchor sequence-mediated conjunction is not located in a promoter; wherein the anchor sequence comprises a CTCF binding site; wherein the anchor sequence is associated with a nucleotide repeat; and wherein the nucleotide repeat is associated with a disease, wherein the disease is chosen from Huntington's Disease, DRPLA (Dentatorubropallidoluysian atrophy), SBMA (Spinal and bulbar muscular atrophy), SCA1 (Spinocerebellar ataxia Type 1), SCA2 (Spinocerebellar ataxia Type 2), SCA3 (Spinocerebellar ataxia Type 3), SCA6 (Spinocerebellar ataxia Type 6), SCAT (Spinocerebellar ataxia Type 7), SCA17 (Spinocerebellar ataxia Type 17), FRDA (Friedreich's ataxia), DM (Myotonic dystrophy), SCA8 (Spinocerebellar ataxia Type 8) or SCA12 (Spinocerebellar ataxia Type 12). 
 
     
     
       2. The chimeric protein of  claim 1 , which epigenetically modifies the anchor sequence. 
     
     
       3. The chimeric protein of  claim 1 , which increases methylation of the anchor sequence. 
     
     
       4. The chimeric protein of  claim 3 , wherein the increase in methylation of the anchor sequence decreases binding of a nucleating protein to the anchor sequence. 
     
     
       5. The chimeric protein of  claim 1 , which modulates the activity and/or expression of one or more target nucleic acid sequences. 
     
     
       6. The chimeric protein of  claim 1 , wherein the anchor sequence is a CTCF binding site. 
     
     
       7. The chimeric protein of  claim 4 , wherein the nucleating protein is CTCF. 
     
     
       8. The chimeric protein of  claim 1 , wherein the epigenetic modifying agent comprises an agent that affects DNA methylation. 
     
     
       9. The chimeric protein of  claim 1 , wherein the epigenetic modifying agent comprises a DNA methylase. 
     
     
       10. The chimeric protein of  claim 9 , wherein the epigenetic modifying agent comprises DNMT3a, DNMT3b, or DNMTL. 
     
     
       11. The chimeric protein of  claim 1 , wherein the epigenetic modifying agent comprises a KRAB domain. 
     
     
       12. The chimeric protein of  claim 1 , wherein the targeting element comprises Cas9. 
     
     
       13. The chimeric protein of  claim 1 , wherein the targeting element comprises a catalytically inactive endonuclease. 
     
     
       14. The chimeric protein of  claim 13 , wherein the catalytically inactive endonuclease comprises dead Cas9 (dCas9). 
     
     
       15. The chimeric protein of  claim 1 , wherein the targeting element further comprises a guide RNA or nucleic acid encoding the guide RNA. 
     
     
       16. The chimeric protein of  claim 15 , wherein the guide RNA comprises a specific targeting sequence for an anchor sequence associated with nucleotide repeat associated with a disease. 
     
     
       17. The chimeric protein of  claim 1 , wherein the targeting element comprises a TALEN domain. 
     
     
       18. The chimeric protein of  claim 1 , wherein the targeting element targets one or more DNA methylation sites within the anchor sequence-mediated conjunction. 
     
     
       19. The chimeric protein of  claim 1 , wherein the chimeric protein modifies binding affinity of the anchor sequence for the nucleating polypeptide. 
     
     
       20. A pharmaceutical composition comprising the chimeric protein of  claim 1  and a pharmaceutically acceptable excipient. 
     
     
       21. The chimeric protein of  claim 1 , wherein the targeting element comprises a zinc finger domain.